test: reorganize test structure and add missing unit tests

Reorganize flat tests/ directory to mirror source code structure
(tools/, gateway/, hermes_cli/, integration/). Add 11 new test files
covering previously untested modules: registry, patch_parser,
fuzzy_match, todo_tool, approval, file_tools, gateway session/config/
delivery, and hermes_cli config/models. Total: 147 unit tests passing,
9 integration tests gated behind pytest marker.

tests/tools/test_todo_tool.py

@@ -0,0 +1,101 @@
+"""Tests for the todo tool module."""
+
+import json
+
+from tools.todo_tool import TodoStore, todo_tool
+
+
+class TestWriteAndRead:
+    def test_write_replaces_list(self):
+        store = TodoStore()
+        items = [
+            {"id": "1", "content": "First task", "status": "pending"},
+            {"id": "2", "content": "Second task", "status": "in_progress"},
+        ]
+        result = store.write(items)
+        assert len(result) == 2
+        assert result[0]["id"] == "1"
+        assert result[1]["status"] == "in_progress"
+
+    def test_read_returns_copy(self):
+        store = TodoStore()
+        store.write([{"id": "1", "content": "Task", "status": "pending"}])
+        items = store.read()
+        items[0]["content"] = "MUTATED"
+        assert store.read()[0]["content"] == "Task"
+
+
+class TestHasItems:
+    def test_empty_store(self):
+        store = TodoStore()
+        assert store.has_items() is False
+
+    def test_non_empty_store(self):
+        store = TodoStore()
+        store.write([{"id": "1", "content": "x", "status": "pending"}])
+        assert store.has_items() is True
+
+
+class TestFormatForInjection:
+    def test_empty_returns_none(self):
+        store = TodoStore()
+        assert store.format_for_injection() is None
+
+    def test_non_empty_has_markers(self):
+        store = TodoStore()
+        store.write([
+            {"id": "1", "content": "Do thing", "status": "completed"},
+            {"id": "2", "content": "Next", "status": "pending"},
+        ])
+        text = store.format_for_injection()
+        assert "[x]" in text
+        assert "[ ]" in text
+        assert "Do thing" in text
+        assert "context compression" in text.lower()
+
+
+class TestMergeMode:
+    def test_update_existing_by_id(self):
+        store = TodoStore()
+        store.write([
+            {"id": "1", "content": "Original", "status": "pending"},
+        ])
+        store.write(
+            [{"id": "1", "status": "completed"}],
+            merge=True,
+        )
+        items = store.read()
+        assert len(items) == 1
+        assert items[0]["status"] == "completed"
+        assert items[0]["content"] == "Original"
+
+    def test_merge_appends_new(self):
+        store = TodoStore()
+        store.write([{"id": "1", "content": "First", "status": "pending"}])
+        store.write(
+            [{"id": "2", "content": "Second", "status": "pending"}],
+            merge=True,
+        )
+        items = store.read()
+        assert len(items) == 2
+
+
+class TestTodoToolFunction:
+    def test_read_mode(self):
+        store = TodoStore()
+        store.write([{"id": "1", "content": "Task", "status": "pending"}])
+        result = json.loads(todo_tool(store=store))
+        assert result["summary"]["total"] == 1
+        assert result["summary"]["pending"] == 1
+
+    def test_write_mode(self):
+        store = TodoStore()
+        result = json.loads(todo_tool(
+            todos=[{"id": "1", "content": "New", "status": "in_progress"}],
+            store=store,
+        ))
+        assert result["summary"]["in_progress"] == 1
+
+    def test_no_store_returns_error(self):
+        result = json.loads(todo_tool())
+        assert "error" in result